TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv2740/ephG:

update plot	correlation	link to info on gene
Rv3165c/-	(cc=0.4995)	info on Rv3165c/-
Rv2060/-	(cc=0.4512)	info on Rv2060/-
Rv2308/-	(cc=0.4399)	info on Rv2308/-
Rv1218c/-	(cc=0.4285)	info on Rv1218c/-
Rv2040c/-	(cc=0.4014)	info on Rv2040c/-
Rv1954A/-	(cc=0.3991)	info on Rv1954A/-
Rv1353c/-	(cc=0.3983)	info on Rv1353c/-
Rv2408/PE24	(cc=0.3907)	info on Rv2408/PE24
Rv1496/-	(cc=0.3907)	info on Rv1496/-
Rv2252/-	(cc=0.3881)	info on Rv2252/-

Correlation of Rv2740/ephG with Rv3165c/-

Normalized LFCs for Rv2740/ephG:
(description and provenance of datasets)

	Rv2740/ephG	Rv3165c/-
Fe_supp_jason_reseq	0.23	1.427
low_pH_jason_reseq	-0.579	0.151
NO_jason_reseq	-0.735	-1.394
B6_jason_reseq	-0.318	0.333
MHCII_jason_reseq	0.109	0.308
Isoniazid02	-0.389	-0.295
Rifampicin4	-0.127	-0.309
Ethambutol3	-0.264	-0.652
Meropenem3	-0.299	0.024
Vancomycin16	-0.631	0.027
Rv2680_day32	1.128	2.941
H37Rv_KO_MarP	-0.292	0.684
hypoxia_3wks	-0.67	-0.327
hypoxia_6wks	-0.238	-0.503
glycerol	-0.307	0.718
cholesterol	-0.285	-0.506
AJ	-0.183	0.128
Bibs02	-0.585	-0.603
Bibs02c	-0.77	-1.291
BL6	-0.372	-0.342
BL6a	0.281	0.161
BXD01	-0.235	0.173
BXD010	0.365	1.189
BXD011	0.709	0.478
BXD03	0.492	0.706
BXD04	-0.043	0.913
BXD05	0.429	-0.249
BXD06	0.072	0.829
BXD07	0.409	0.687
BXD08	0.616	0.143
BXD09	0.427	0.486
CAST	0.327	0.305
CCcont	-0.113	0.661
DS01	-1.258	-0.32
DS02	-1.3	-2.757
DS04	0.066	-1.577
DS0c	-0.757	-0.715
GP01	0.403	-0.715
GP02	0.014	-1.448
GP0c	0.834	-0.98
NOD	-0.135	-0.199
NZO	0.428	0.564
PWK	-0.675	0.159
H37Rv_KO_CtpC	-0.598	-0.567
H37Rv_KO_CtpD	0.479	1.921
H37Rv_KO_Rv1272	0.103	-0.082
H37Rv_KO_SugABC	-2.096	-0.562
H37Rv_KO_MbtN	-0.306	0.877
Trans05	0.053	1.323
macrophage_unactivated	-0.227	1.266
IL1	0.448	1.023
Rapamycin	0.672	0.657
Tcell	-0.635	0.896
GMCSF	0.734	1.766
IFNab	0.36	0.686
IFNg	0.222	1.406
IFNg_GMCSF1	-0.544	0.0
Rv1432_day32	-0.327	-1.042
Rv1565c_day32	0.826	1.567
secA2_input	-2.057	0.18
delta_Rv3594	0.217	-0.529
delta_Rv3717	1.121	-0.062
delta_Rv3811	-0.311	0.568
delta_Rv0954	-1.55	-1.112
PonA1	0.187	-1.602
EccD1_KO	1.217	0.414
EspI_KO	0.704	1.198
PE35_KO	0.933	0.84
PPE68_KO	1.094	0.771
glycerol2	0.404	0.717
lignocerate	0.479	1.492
oleate	-0.713	-3.549
phosphatidylcholine	0.625	0.378
acetate	0.356	1.197
glucAc	0.869	1.646
Rv0950ko	0.241	0.265
Rv1096ko	0.47	0.09
Rv3684ko	-0.174	-0.049
delta_otsA_trehalose	0.404	0.111